Biological Assembly 1  

 3D View: Structure | Electron Density | Ligand Interaction

Global Symmetry: Cyclic - C2  (3D View)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 26.16 kDa 
• Atom Count: 1918 
• Residue Count: 209 
• Unique protein chains: 1

5NYH

Crystal Structure of Hsp90-alpha N-Domain in complex with Indazole derivative

• DOI: 10.2210/pdb5NYH/pdb

• Classification: CHAPERONE
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2017-05-11 Released: 2018-04-18 
• Deposition Author(s): Amaral, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.226 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 

Literature

Ligand Desolvation Steers On-Rate and Impacts Drug Residence Time of Heat Shock Protein 90 (Hsp90) Inhibitors.

Schuetz, D.A., Richter, L., Amaral, M., Grandits, M., Gradler, U., Musil, D., Buchstaller, H.P., Eggenweiler, H.M., Frech, M., Ecker, G.F.

(2018) J Med Chem 61: 4397-4411

• PubMed: 29701469 
• DOI: 10.1021/acs.jmedchem.8b00080
• Primary Citation of Related Structures:  
  5LO1, 5LO0, 5LNZ, 5LNY, 5OD7, 5OCI, 5ODX, 5NYH


• PubMed Abstract: 
  

Residence time and more recently the association rate constant k _on are increasingly acknowledged as important parameters for in vivo efficacy and safety of drugs. However, their broader consideration in drug development is limited by a lack of knowledge of how to optimize these parameters. In this study on a set of 176 heat shock protein 90 inhibitors, structure-kinetic relationships, X-ray crystallography, and molecular dynamics simulations were combined to retrieve a concrete scheme of how to rationally slow down on-rates. We discovered that an increased ligand desolvation barrier by introducing polar substituents resulted in a significant k _on decrease. The slowdown was accomplished by introducing polar moieties to those parts of the ligand that point toward a hydrophobic cavity. We validated this scheme by increasing polarity of three Hsp90 inhibitors and observed a 9-, 13-, and 45-fold slowdown of on-rates and a 9-fold prolongation in residence time. This prolongation was driven by transition state destabilization rather than ground state stabilization.

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Organizational Affiliation: 

Department of Pharmaceutical Chemistry , University of Vienna , UZA 2, Althanstrasse 14 , 1090 Vienna , Austria.

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Heat shock protein HSP 90-alpha	A	229	Homo sapiens	Mutation(s): 0  Gene Names: HSP90AA1, HSP90A, HSPC1, HSPCA
Find proteins for P07900 (Homo sapiens) Explore P07900  Go to UniProtKB:  P07900
NIH Common Fund Data Resources
PHAROS:  P07900 GTEx:  ENSG00000080824

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
9EK	A	~{N}-methyl-~{N}-(4-morpholin-4-ylphenyl)-6-oxidanyl-3-pyrrolidin-1-ylcarbonyl-2~{H}-indazole-5-carboxamide C24 H27 N5 O4 PAGPOZMFSDBEOC-UHFFFAOYSA-N

External Ligand Annotations
ID	Binding Affinity (Sequence Identity %)
9EK	Kd:  18.700000762939453   nM  Binding MOAD

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.65 Å
• R-Value Free: 0.226 
• R-Value Work: 0.207 
• R-Value Observed: 0.208 
• Space Group: I 2 2 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 69.979	α = 90
b = 88.54	β = 90
c = 97.091	γ = 90

Software Package:

Software Name	Purpose
BUSTER	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Deposited Date: 2017-05-11 
• Released Date: 2018-04-18 
Deposition Author(s): Amaral, M.

Revision History 

• Version 1.0: 2018-04-18
  Type: Initial release
  
• Version 1.1: 2018-05-23
  Changes: Data collection, Database references
• Version 1.2: 2018-06-06
  Changes: Data collection, Database references